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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Added output filename argument #28

Closed ssnn-airr closed 6 years ago

ssnn-airr commented 9 years ago

Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

We might want to allow overwrite of the input file and/or explicit specification of the output file name with an optional --overwrite argument. We would have to write to a tempfile, then move the tempfile after the task is done, but that shouldn't require much of a change if we tie it to an optional argument.

ssnn-airr commented 6 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Well that was tedious. Done in d069248. Still needs some testing though.

ssnn-airr commented 6 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Okay, I'm going to go with "no" on the --overwrite argument, but we can add an explicit output file name argument instead (as per -o in changeo). At the same time, we can do #62 as well as swap things to the simpler interface that doesn't load everything into SeqRecord objects.